Download Review of Contractor Data

Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
Procedure for GeneMapper® ID
1.0
Purpose – This procedure specifies the steps for performing analysis on DNA samples using
GeneMapper® ID (GMID) software.
2.0
Scope – This procedure applies to Forensic Scientists and Database Analysts in the Forensic Biology
Section who perform DNA analysis using GMID.
3.0
Definitions
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
4.0
Equipment and Materials
•
•
•
5.0
Amelogenin - Gender-determining short tandem repeat (STR) locus.
Artifact - See Forensic Biology Section Autosomal DNA STR Interpretation Procedure.
Bin - An expected location for a particular allele within a locus; a binset is a collection of expected
locations for alleles at loci amplified as a set.
Consensus Allele - An allele that conforms to an incremental repeat pattern at an STR locus.
Electropherogram (egram) - The computer generated electronic/visual result from an analysis
performed by electrophoresis.
.fsa File - A raw data file generated during sample electrophoresis as part of a run; only viewable
through GMID software (or equivalent).
Heterozygote Peak Imbalance - A difference of greater than approximately 50% between two
peaks of a single source sample at a given locus.
Identifiler™ - A commercially produced amplification kit which contains the following STRs:
CSF1PO, FGA, THO1, TPOX, vWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539,
D18S51, D21S11, D2S1338, D19S433, and Amelogenin.
Injection - See Forensic Biology Section Autosomal DNA STR Interpretation Procedure.
LIZ Sizing Standard - A commercially produced set of DNA fragments of known size, used to
determine the size of DNA fragments in an electrophoresed sample.
Locus (plural, loci) - See Forensic Biology Section Autosomal DNA STR Interpretation Procedure;
also referred to as a marker.
Microvariant - See Forensic Biology Section Autosomal DNA STR Interpretation Procedure.
Off Ladder Allele - See Forensic Biology Section Autosomal DNA STR Interpretation Procedure.
Overblown/Off-Scale Data - See Forensic Biology Section Autosomal DNA STR Interpretation
Procedure.
Panel - A collection of markers specific to an amplification kit (i.e., Identifiler™).
Project - A set of data saved as a single entity in GMID.
Relative Fluorescence Units (RFUs) - A unit of measurement used in electrophoresis when
fluorescence detection is utilized; determines peak height.
Run - See Forensic Biology Section Autosomal DNA STR Interpretation Procedure.
Split Peaks - See Forensic Biology Section Autosomal DNA STR Interpretation Procedure.
Computer with GeneMapper® ID (version 3.2.1 or most current) software
Microsoft Excel, Word
Print2PDF software
Procedure
Page 1 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
5.1 Setting Analysis Parameters for GMID: Each user shall import from the Section Shared Drive the
following files as required for the type of analysis being performed into his/her copy of GMID prior
to analysis (if not already present):
5.1.1
Analysis Methods:
•
•
•
5.1.2
G5_Advanced.xml
NCSBI Robot.xml (Database Robot runs only)
North Carolina v2.xml (Database Contractor Data Review only, provided by contract
laboratory)
Panels/Bins:
•
•
•
AmpFLSTR_Panels_v2.txt
AmpFLSTR_Panels_v2_AmpFLSTR_Bins_v2_bins.txt
AmpFLSTR_Panels_NC_v2_Panels.txt (Database Contractor Data Review only,
provided by contract laboratory)
AmpFLSTR_Panels_NC_v2_AmpFLSTR_Bins_NC_v2_bins.txt (Database Contractor
Data Review only, provided by contract laboratory)
•
5.1.3
Size Standards:
•
5.1.4
GS500LIZ_Advanced.xml
Tables and Plot Settings:
•
•
•
•
•
•
•
SBI Casework Table.xml
AmpFLSTR Sizing plot.xml
Case Allele Table.xml
Overlay LIZ plot.xml
AmpFLSTR Genotyping plot.xml
AmpFLSTR Table.xml
CODIS Export Table.xml
5.2 Creating a Project
5.2.1
Open GMID and log in under Forensic Scientist’s/Database Analyst’s name/log-in.
Analysis under the generic “gmid” log-in name is not permitted.
5.2.2
For Database review of contractor data, the contractor-provided .ser file(s) shall be
imported using GeneMapper Manager. The following files must be added to GMID prior
to review:
•
•
Analysis Method: North Carolina v2.xml
Panels/Bins: AmpFLSTR_Panels_NC_v2_Panels.txt and AmpFLSTR_Panels_NCv2_AmpFLSTR_Bins_NC_v2.bins.txt
Refer to DNA Database Review of Contractor Data for review procedure.
5.2.3
Select “File” and “Add samples to project.”
Page 2 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
5.2.4
Locate the run folder containing the samples to be added to the project under the “Files”
tab. Highlight the run folder (or select the specific samples to be analyzed) and select
“Add to List.” The file(s) then appears on the right-hand side. Select “Add.”
5.2.5
In the Samples pane, the category “Sample Type” shall have the samples labeled as
follows when amplified with Identifiler™:
•
•
•
•
•
5.2.6
The remaining categories shall be filled out as follows:
•
•
•
•
•
5.2.7
Ladder: Allelic Ladder
9947A (Positive Amplification Control): Positive Control
Negative Amplification Control: Negative Control
All other samples shall be “Samples”
Note: Sample File names appear by well number (ie, A12) followed by the sample
name as entered by the Forensic Scientist/Database Analyst prior to electrophoresis.
Also, until the samples are analyzed, the “Status” icon to the left of the Sample File
name has the unanalyzed icon (
) present next to it. If no “Status” category or
icons are present, verify that the table setting (in top center of the main GMID
window) is set to “AmpFLSTR Table.”
Specimen Category: no export
Analysis Method: G5_Advanced or NCSBI Robot (for Robot runs)
Panel: Identifiler_v2
Size Standard: GS500LIZ_Advanced
Instrument Type: ABI3130, or similar (note: automatically filled in by the software
and instrument)
Once all samples and categories are properly labeled and identified, select the “Analyze”
icon ( ) to analyze the data. When prompted, create a project name for the set of
samples and select “Save.”
5.2.7.1 Note: GMID auto-saves data after every 10 samples have been processed.
5.2.7.2 Note: The Genotypes tab becomes available in the main GMID window once
analysis is complete.
5.2.7.3 Note: If any sample displays a solid red “stop” sign icon ( ) on the right-hand
side of the GMID window, assess the data as described in 5.3.
5.2.8
Analysis and Plot Settings
5.2.8.1 Access the Analysis Method Editor by selecting “Analysis” from the menu in the
main GMID window, and then select “Analysis Method Editor.” Note that the
user must have a single sample in the main GMID window selected in order to
access the Editor.
5.2.8.2 Select the “Peak Detector” tab, and for casework ensure that the settings are as
seen below when the samples have been amplified with Identifiler™. Note that
the Peak Threshold is set to 75 for the blue, green, yellow and red channels for
Page 3 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
casework. Note that the threshold for orange (LIZ) is set to 80 RFU for all
casework and database samples.
For Database samples generated in-house, the Peak Threshold for the blue, green,
yellow and red channels shall be set according to the screenshot below.
Page 4 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
For Database robot samples, the Peak Threshold for the blue, green, yellow and
red channels shall be set according to the screenshot below.
Page 5 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
For Database samples generated by contractors, the Peak Threshold for the blue,
green, yellow and red channels shall be set according to the screenshot below.
Page 6 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
5.2.8.3 Next select the “Allele” tab; the contents should appear as below:
Page 7 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
5.2.8.4 In the main GMID window, select “Tools” from the top menu, and then select
“Table Setting Editor.” Under the “Genotypes” tab, at the bottom of the window,
ensure that the “Number of Alleles” under “Allele Settings” is set to at least 12
for casework. Forensic Scientists/Database Analysts may adjust this number if
necessary (i.e., to maximum number of called allele at any locus).
5.2.9
Adding/Deleting samples
5.2.9.1 If a Forensic Scientist/Database Analyst must add an additional sample(s) to a
current project, follow 5.2.3 through 5.2.8. The newly added sample shall be
analyzed (select the “Analyze” icon) before the data can be viewed.
5.2.9.1.1 Note: if the sample is from a different injection (i.e., run folder), the
associated Allelic ladder shall also be imported in order for the sample
data to be sized properly.
5.2.9.2 If a Forensic Scientist/Database Analyst must remove a sample(s) that has been
added to the project (i.e., a sample from an unrelated case or CODIS
confirmation), highlight the sample to be removed and in the menu bar, select
“Edit” and “Delete from Project.” Select “OK” when prompted.
5.2.9.2.1 Note: samples from the same case or confirmation that are present in a
project but are not used (i.e., redundancy, sizing data issues, or similar)
shall not be deleted (refer to 5.3.2.3.2).
5.3 Analyzing/Preliminary Evaluation of Data of Each GMID Project
5.3.1
Evaluate Sizing Data (i.e., LIZ)
5.3.1.1 Select “Edit” from the GMID menu bar at the top of the window and “Select
All.” Click on the Size Match Editor icon ( ). The new window that opens
Page 8 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
displays the LIZ sizing data for all selected samples; scroll through each one and
confirm that all sizing peaks are correct (75, 100, 139, 150, 160, 200, 300, 340,
350, 400, and 450- base pairs). Close this window.
5.3.1.1.1 Note: If all peaks are not called, the analysis range may need to be
extended: view the Analysis Settings in 5.2.8. 2 and change the analysis
range to “Full Range” in the “Peak Detector” tab.
5.3.1.2 Again select all the samples in the main GMID window and select the “Display
Plots” icon ( ). This opens the Sample Plot window for all selected samples.
Change the Plot Setting to “Overlay LIZ” by selecting it from the dropdown
menu in the top left portion of the Sample Plot window. Zoom in to the area near
the 250-base pair peak (bp) by holding the mouse just above the horizontal scale,
indicating bp size, and then clicking and dragging to zoom.
5.3.1.2.1 Note: the 250-bp peak was not defined by the manufacturer in the size
standard. The purpose of checking this sizing peak is to determine if
the 250-bp peak within the samples and controls are within +/- 0.5 bp
of the 250-bp sizing peak of the allelic ladder they were injected with.
Therefore, no sample or control run in-house shall be used for analysis
if its 250-bp peak falls outside of this window in relation to the allelic
ladder. Any sample or control that exceeds the window shall be reinjected (refer to the Forensic Biology Section Procedure for Use of the
3130XL Genetic Analyzer for reinjection requirements).
5.3.1.3 Highlight the 250-bp peak and hold down the Ctrl and “S” key on the keyboard
to select all samples at the 250-bp peak. The sizing table then displays the 250-bp
peak size for all selected samples. If any sample has a 250-bp peak which is
greater than +/- 0.5 bp from the 250-bp peak in the associated allelic ladder, refer
to 5.3.1.2.1.
5.3.1.4 If any sample or control in the project indicates “no sizing data” (i.e., LIZ
failure), then that sample or control shall not be used for comparison and shall be
re-injected to achieve proper sizing information. This information shall be noted
on the Casework Table Worksheet. If there is no sizing data for an allelic ladder,
then no data associated with that ladder can be sized and the entire set shall be reinjected.
5.3.2
Assess Overall Quality of Data
5.3.2.1 Allelic Ladders and Controls
5.3.2.1.1 In the main GMID window, select the allelic ladder(s) and open the
sample plot window by selecting the “Display Plots” icon. In the
Samples Plot window, ensure that the Plot Setting is set to
“AmpFLSTR Genotyping.”
Page 9 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
5.3.2.1.2 Scroll through each of the color channels (blue, green, yellow, red) and
verify that all the alleles are sized and labeled correctly according to
the expected calls for the Identifiler™ Allelic ladder. All expected
peaks must be present and above the appropriate analytical threshold
(i.e., database or casework thresholds). Close this Sample Plot window.
5.3.2.1.3 In the main GMID window, select the positive and negative
amplification and extraction controls if used. Open the sample plot
window as described previously.
5.3.2.1.4 Examine the positive control(s) for the expected allelic results and to
ensure that the negative controls meet the required interpretive
guidelines (see the Forensic Biology Section Procedure for Autosomal
DNA STR Interpretation). Remove any artifacts as described in
5.3.2.2.1.1. Close the Sample Plot window.
5.3.2.2 Samples
5.3.2.2.1 Examine all samples in the manner as described for the allelic ladders
and controls.
5.3.2.2.1.1 Artifacts: If any peaks are to be removed from
consideration as true alleles due their presence as a known
artifact (i.e., pull-up, dye-blob, stutter, spike), highlight the
sizing box associated with the peak and right-click the
mouse. Select “Delete Allele(s)” (multiple peaks can be
deleted simultaneously by selecting them at the same
time—when the warning dialog box appears, select “OK”).
When prompted by the “Delete Allele Comment,” type in
“artifact” and the Forensic Scientist’s/Database Analyst’s
initials.
5.3.2.2.1.2 Microvariants: If a microvariant is present in a sample and
GMID has not automatically assigned it an allelic value,
Forensic Scientists/Database Analysts shall document the
proper sizing of the microvariant as follows:
5.3.2.2.1.2.1 In the main GMID window, select the
sample(s) containing the microvariant and the
allelic ladder. Display Plots. Zoom in to the
locus containing the microvariant; the Sample
Plot displays the allelic ladder in the top half
of the Plot window and the sample is in the
bottom half.
5.3.2.2.1.2.2 Highlight the microvariant in the sample,
along with the alleles in the allelic ladder that
lie the closest in size to the microvariant (to
Page 10 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
select peaks simultaneously, hold down the
Ctrl key on the keyboard while selecting).
Select the sizing table icon (
). Select Ctrl
+ S to make the sizing table display the
selected alleles.
5.3.2.2.1.2.3 Based upon the sizing information provided in
the table, determine the appropriate allele call
for the microvariant. For CODIS eligibility,
refer to the Procedure for CODIS.
5.3.2.2.1.2.3.1 Note: the correct allele call for
the microvariant is dependent
upon the microvariant’s base
pair size when compared to the
allelic ladder.
5.3.2.2.1.2.3.2 Note: microvariants that vary
by less than the consensus
repeat unit for that locus must
be designated as an integer of
that variation (i.e., the 9.3
allele at TH01).
5.3.2.2.1.2.4 Rename the allele by right-clicking on it and
selecting “Rename Allele.” If the correct
allele call is not already present in the
subsequent drop-down list, select “Custom”
and enter the call in the “Create Custom Allele
Name” box. When prompted by the “Edit
Allele Comment” box, type in “microvariant”
and
the
Forensic
Scientist’s/Database
Analyst’s initials.
5.3.2.2.1.2.5 With the alleles highlighted in 5.3.2.2.1.2.2
still present in the sizing table (remove any
extraneous), select “File” and “Print” and
select “Print2PDF.”
5.3.2.2.1.2.6 In casework samples, if a microvariant is
observed in a single instance in a case, it shall
be reamplified to verify its presence in the
sample. If the microvariant is observed
throughout the case, across more than one
sample (question or known), then the
sample(s) containing the microvariant do not
need to be re-amplified. For database samples,
Page 11 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
re-amplification or re-extraction of the sample
shall be at the Forensic Scientist’s/Database
Analyst’s discretion (see the Forensic Biology
Section DNA Database procedures).
5.3.2.2.1.3 Off Ladder Alleles: If a sample(s) contains an off ladder
allele that is not an artifact, the Forensic Scientist/Database
Analyst shall assign the allele to the correct locus if possible
(see below). For CODIS eligibility, refer to the Forensic
Biology Section Procedure for CODIS.
5.3.2.2.1.3.1.1 If the allele in question lies between two
loci, the Forensic Scientist/Database Analyst
shall attempt to determine which locus the
allele should be assigned to based upon the
presence or absence of heterozygosity at the
loci in question.
5.3.2.2.1.3.1.2 If one locus exhibits homozygosity and the
second heterozygosity, the off ladder allele
shall be assigned to the homozygous locus.
5.3.2.2.1.3.1.3 If both loci exhibit homozygosity or
heterozygosity,
the
Forensic
Scientist/Database Analyst shall document
either on the allele call table or the
electropherograms that the allele was
observed, but not assign the allele to a
particular locus, and mark the allele as
inconclusive (INC). The called (non off
ladder) alleles at these loci shall be reported
and uploaded into CODIS.
5.3.2.2.1.3.1.4 Note: In some instances, an off ladder allele
from one locus may appear within an
adjacent locus (i.e., appears to be a potential
triallele next to a homozygous locus). If
based on training and experience, the
Forensic Scientist/Database Analyst believes
such a situation has occurred, the entire
locus containing that allele may be marked
as inconclusive.
5.3.2.2.1.3.2 If the off ladder allele can be assigned to a locus,
the allele must be designated as either greater than
(>) or less than (<) the last respective allele for that
locus called by the allelic ladder. For CODIS
Page 12 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
eligibility, refer to the Forensic Biology Section
Procedure for CODIS.
5.3.2.2.1.3.3 Follow the steps outlined for microvariants for
assigning a value to the off ladder allele, as well as
the printing format, with the exception that the
“comment” shall be “off ladder allele” instead of
“microvariant.”
5.3.2.2.1.3.4 In casework samples, if an off ladder allele occurs
as a single instance, it shall be re-amplified. In
database samples, re-amplification or re-extraction
shall be at the Forensic Scientist’s/Database
Analyst’s discretion (see 5.3.2.2.1.2.6).
5.3.2.2.1.3.5 If the GMID software does not allow the Forensic
Scientist/Database Analyst to assign a value to the
off ladder allele, the Forensic Scientist/Database
Analyst shall follow the same procedure for
documentation and assignment of microvariants.
The Forensic Scientist/Database Analyst shall be
required to print out the sizing table/egram
combination and manually write the proper sizing
designation to the off ladder allele along with the
Forensic Scientist’s/Database Analyst’s initials.
These pages shall then be scanned into PDF format.
5.3.2.2.1.3.5.1 Note: the Allele Call Table
Worksheet also needs to be
changed to reflect the proper allele
call for the off ladder allele that
cannot be exported through the
GMID software.
5.3.2.2.1.4 Sizing Shifts: If any allele at any locus has been sized outside
of the appropriate bin which results in an “off ladder” call by
GMID, the sample shall be re-injected (or re-amplified, if
necessary) in order to size the allele(s) properly if the
Forensic Scientist/Database Analyst wants to use the results at
that locus. Shifted alleles/loci shall not be used for
comparison in any control, ladder or sample.
5.3.2.2.1.5 Overblown/Off-scale Samples: overblown samples in
casework shall not be used for comparison. Such samples
shall be either re-injected for a lower injection time (i.e., 22 to
10 seconds) or re-amplified with a lower concentration. The
use of overblown samples in Database samples shall be at the
Page 13 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
discretion of the Forensic Scientist/Database Analyst based
upon the training and experience of the Forensic
Scientist/Database Analyst.
5.3.2.2.1.6 Tri-alleles: For casework, the sample shall be re-extracted
unless the tri-allelic pattern appears at least twice within a
case. For database, the sample shall be re-extracted except in
CODIS confirmations.
5.3.2.3 Printing Egrams Electronically
5.3.2.3.1 All egrams shall be printed using the Print2PDF printer, with the
exception of 5.3.2.2.1.3.5. The egrams for each GMID project shall
exist as its own PDF file.
5.3.2.3.1.1 Note: GMID projects are added to the FA case record
object repository by exporting the projects: in GMID, select
“Tools,” “GeneMapper Manager,” select the applicable
project and select “export.” The file is exported/saved as an
.ser file.
5.3.2.3.2 Any individual sample/control/ladder with the case or CODIS
confirmation that is not used for comparison purposes (i.e., LIZ failure,
redundancy, further analysis) shall be printed in PDF format. Such
samples/controls/ladders shall appear in the Casework Table explaining
it was not used for comparison (e.g., LIZ failure, redundancy, reanalysis).
5.3.2.3.2.1 Note: Even if not used for comparison purposes, all .fsa
files associated with such samples/controls/ladders shall be
present in the run folder containing the electronic data in
the FA case record object repository.
5.3.2.3.2.2 Note: For any sample/control/ladder that is not used for
comparison purposes, corrections (labeling of artifacts) are
not required.
5.3.2.3.3 If an entire run or project for a case or CODIS confirmation is not used
for comparison purposes, it shall be printed as Print2PDF and added to
the case record object repository. Corrections (i.e., labeling of
artifacts) are not required in this instance. A Casework Table shall be
generated for this instance and the reason for not using the entire
run/project shall be noted on this page (also Print2PDF; see 5.4.1). An
Allele Call Table is not required for such runs/projects.
5.3.2.3.4 The LIZ sizing standard shall be printed (Print2PDF) as a separate set
of egrams which may be added to the overall egram PDF file for each
project, or kept separately as an independent document. The LIZ must
Page 14 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
be present for all samples/controls/ladders and all peaks (75 through
450) must be visible.
5.3.3
View Raw Data
5.3.3.1 In order to verify the addition of amplification kit primers to all negative controls
and negative samples (which includes instances of LIZ or injection failure), the
raw data for such samples from each project must be present in each case record
object repository.
5.3.3.1.1 In the main GMID window, highlight the negative control or negative
sample and select “Raw Data” from the “View” option in the main
GMID menu.
5.3.3.1.2 The subsequent window displays the raw data on the right-hand side
and the sample and run information on the left-hand side. Expand the
left-hand window so that the full run file name (including run number)
is clearly visible. The right-hand window shall show the maximum
vertical and horizontal axis.
5.3.3.1.3 Using the Alt + Print Screen buttons on the computer, take a
“snapshot” of the raw data window. Open up a Word document and
paste this “snapshot” into the document. Repeat this process for all
negative samples and negative controls in each project.
5.3.3.1.3.1 This raw data Word document shall contain at least the
following information in the header: full case number (or
batch number for Database; refer to the DNA Database
Procedures), date, Forensic Scientist’s/Database Analyst’s
initials.
5.3.3.1.4 The Word document(s) containing the “snapshots” of the raw data shall
be included in the scanned or Print2PDF case notes.
5.4 Exporting and Creating Tables
5.4.1
Casework Table
5.4.1.1 In the main GMID window, select the “SBI Casework Table” from the Table
Setting menu.
5.4.1.2 Select all samples and under “File” in the main GMID menu, select “Export
Table.” Save the table to a location easily located by the Forensic
Scientist/Database Analyst (i.e., desktop or thumb drive). Ensure the file is
exported/saved in the “Tab- and Comma-delimited Text” (.txt) format.
5.4.1.3 Open Excel; open the .txt file saved in the previous step (note: the Forensic
Scientist/Database Analyst may have to change the “files of type” to “All Files”
in order for the software to access the .txt file).
Page 15 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
5.4.1.4 When the Text Import Wizard opens, select “Finish.”
5.4.1.5 Adjust the columns to accommodate the full text for each line.
5.4.1.6 Select “Page Setup.” Under the “Page” tab, select “landscape” and fit to 1 page
wide by 1 page tall; under the “Header/Footer” tab, select “Custom Header”—at
a minimum, the Forensic Scientist/Database Analyst shall enter the full case
number (or batch number for Database), initials, and the date; under the “Sheet”
tab, select only the “Gridlines” box. Finish by selecting “OK.” Alternately,
Forensic Scientist /Database Analysts may use the Casework Table Worksheet to
create this table.
5.4.1.7 Forensic Scientists/Database Analysts shall note on this page any samples that
are not to be used for comparison and why, or those that are to have additional
analysis performed on them (see 5.3.2.3.2).
5.4.1.8 Print the Casework Table Worksheet by using the Print2PDF printer. The
Casework Table Worksheet shall exist independently of the egrams and the
Allele Call Table Worksheet(s). It may be merged with the set-up sheet.
5.4.1.9 Note: only samples and controls specific to the case or CODIS confirmation shall
be present in the Casework Table.
5.4.2
Allele Call Table
5.4.2.1 In the main GMID window, select the “Case Allele Table” from the Table
Setting menu. With all samples selected, select the “Genotypes” tab in the main
GMID menu.
5.4.2.2 Under the “File” menu in the main GMID window, select “Export Table.” Save
the table to a location easily located by the Forensic Scientist/Database Analyst
on his/her computer (i.e., desktop or thumb drive). Ensure the file is
exported/saved in the “Tab- and Comma-delimited Text” (.txt) format.
5.4.2.2.1 Note: the Forensic Scientist/Database Analyst may need to add
additional information to the .txt file name in order to avoid copying
over the Casework Table file.
5.4.2.3 Open Excel; open the .txt file saved in the previous step (note: the Forensic
Scientist/Database Analyst may have to change the “files of type” to “All Files”
in order for the software to access the .txt file).
5.4.2.4 When the Text Import Wizard opens, select “Finish.”
5.4.2.5 Open the Allele Call Table Excel file in the Forensic Biology Shared Folder. For
Robot runs, use the Robot Allele Call Table. For manual runs performed in the
database, either the Robot Allele Call table or manual allele call table may be
used. Copy and paste the allele calls generated from the .txt file in 5.4.2.4 (Select
“All”) into the “Results” tab in the appropriate Allele Call Table Worksheet.
Page 16 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
5.4.2.6 Return to the “Allele Call Table” tab (or the “Mixture” tabs if any samples have
more than 2 alleles at any given locus) and verify that the copy and paste
function worked properly.
5.4.2.7 If minor alleles or profiles are to be marked, the Forensic Scientist/Database
Analyst shall highlight the cells containing the minor allele/profile. The Forensic
Scientist/Database Analyst shall make a key at the bottom (or in the footer) of the
Allele Call Table indicating what the highlighted cell represents.
5.4.2.8 If multiple injections are present in a case file, the Forensic Scientist/Database
Analyst shall indicate from which run number the sample came. Item
descriptions shall also be typed into the designated areas in the worksheet. The
Forensic Scientist/Database Analyst shall ensure their initials are typed on each
page of the worksheets, as well as the full case number (or batch number for
Database) and the date.
5.4.2.9 In casework, it is permissible for the Forensic Scientist to combine all Allele Call
Table Worksheets into one Excel spreadsheet.
5.4.2.10 In casework, Forensic Scientists shall note any activity or allelic dropout (or
similar notations) on the Allele Call Table Worksheet(s).
5.4.2.11Print the Allele Call Table Worksheet(s) using the Print2PDF printer. This file
must be separate from the file containing the egrams or the Casework Table.
5.4.2.12Note: only samples specific to the case or CODIS confirmation are required to be
present in the Allele Call Table (i.e., controls and ladders).
5.4.3
CODIS Table
5.4.3.1 For casework, refer to the Procedure for CODIS for CODIS Table Export.
5.4.3.2 For casework, refer to the Procedure for CODIS for Specimen Upload.
5.4.3.3 For Database, refer to the Procedure for CODIS, Procedure for DNA Database
Review Contractor Data, and the Procedure for DNA Analysis and Technical
Review of Database Samples for CODIS sample export and specimen upload.
6.0
Limitations – GMID cannot be used on computers operating on Windows 7 or higher.
7.0
Safety – N/A
8.0
References
Applied Biosystems. GeneMapper® ID Software Version 3.1 User’s Guide. P/N 4338775 Rev. C.
Applied Biosystems. AmpFℓSTR® Identifiler™ PCR Amplification Kit User’s Manual. P/N 4323291
Rev. B.
Forensic Biology Section Procedure for Autosomal DNA STR Interpretation
Page 17 of 18
All copies of this document are uncontrolled when printed.
Procedure for GeneMapper® ID
Forensic Biology Section
Version 2
Effective Date: 10/26/2012
Forensic Biology Section Procedure for Use of the 3130XL Genetic Analyzer
Forensic Biology Section Procedure for CODIS
Forensic Biology Section DNA Database Procedures
Forensic Biology Section Procedure for DNA Database Review of Contractor Data
Forensic Biology Section Procedure for DNA Database Analysis and Technical Review of Database
Samples
NDIS STR Data Entry Software (accessible by registered CODIS users only)
9.0
Records
•
•
10.0
Identifiler™ Allelic Ladder Expected Results
Identifiler™ 9947A and MJB Expected Results
Attachments – N/A
Revision History
Effective Date
09/17/2012
10/26/2012
Version Number
Reason
1
Original Document
2
Changed wording in 5.4.2.12 from “shall” to “are required” to allow
analyst to add control results if warranted. Added option to 5.4.2.5 to
allow either the Robot or manual allele call tables to be used for
manual runs in the Database. Added 5.3.2.3.2.2, note to not require
corrections to egrams that are not used for comparisons.
Page 18 of 18
All copies of this document are uncontrolled when printed.